Re: [PyMOL] Question about visualisation of the spheres objects on PNG image
Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd
cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"
Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.
Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?
Cheers,
J.
пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay :
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom
> i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon" wrote:
>
> Dear Pymol Users,
>
> Working on the visualisation of protein-ligand interactions, notably
> focusing on the visualisation of sphres atoms covered protein surface,
> I noticed on the resulted PNG that some sphere objects (located on the
> backing plane) looks VERY small compared to the rest. For example as
> it could be seen while major spheres represent like spheres, some of
> them look like dots, while in the pml session everything looks
> correctly. How could I fix using some pymol settings ?
> Thank you in advance!
> J
>
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Re: [PyMOL] [EXTERNAL] Re: Question about visualisation of the spheres objects on PNG image
Hi Jeff,
In the png file that you posted last week, the smaller spheres
were a lot smaller. They reminded me of nb_spheres.
Did you turn on the display of nb_spheres in your .pymolrc file?
Best regards,
Blaine
From: Jeff Saxon [jmsstarli...@gmail.com]
Sent: Monday, March 01, 2021 4:04 AM
To: Ali Saad Kusay
Cc: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] Question about visualisation of the spheres
objects on PNG image
Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd
cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"
Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.
Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?
Cheers,
J.
пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay :
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom
> i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon" wrote:
>
> Dear Pymol Users,
>
> Working on the visualisation of protein-ligand interactions, notably
> focusing on the visualisation of sphres atoms covered protein surface,
> I noticed on the resulted PNG that some sphere objects (located on the
> backing plane) looks VERY small compared to the rest. For example as
> it could be seen while major spheres represent like spheres, some of
> them look like dots, while in the pml session everything looks
> correctly. How could I fix using some pymol settings ?
> Thank you in advance!
> J
>
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[PyMOL] Ribbon width per residue
Hello, is it possible in Pymol to set the width of the ribbon representation per atom/residue like Chimera does with its ribscale command? Thanks Stefan ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Ribbon width per residue
Hi Stefan, As far as a I know cartoon width settings like "cartoon_oval_length" and "cartoon_oval_width" are object level settings meaning they cannot be implemented on a per residues basis (https://pymolwiki.org/index.php/Cartoon_Helix_Settings). You can use the putty mode which sets width according to b-factors (https://www.pymolwiki.org/index.php/File:B_factor_putty.png) You can set the residue b-factors to any desired per residue width Another way is to use a colour spectrum instead of changing width Let me know if you are interested in either of these approaches and I can help you Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 On 2/3/21, 1:37 am, "achatz" wrote: Hello, is it possible in Pymol to set the width of the ribbon representation per atom/residue like Chimera does with its ribscale command? Thanks Stefan ___ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/OCcaCnx1jniRAJD8t9qlwE?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/rMHzCoV1kpfyj7YOSzndGp?domain=sourceforge.net ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Question about visualisation of the spheres objects on PNG image
Hi Jeff,
That would be cmd.disable("object name") #
https://pymolwiki.org/index.php/Disable
Cheers,
Ali
On 1/3/21, 9:05 pm, "Jeff Saxon" wrote:
Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd
cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"
Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.
Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?
Cheers,
J.
пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay :
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom
i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and
Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon" wrote:
>
> Dear Pymol Users,
>
> Working on the visualisation of protein-ligand interactions, notably
> focusing on the visualisation of sphres atoms covered protein surface,
> I noticed on the resulted PNG that some sphere objects (located on the
> backing plane) looks VERY small compared to the rest. For example as
> it could be seen while major spheres represent like spheres, some of
> them look like dots, while in the pml session everything looks
> correctly. How could I fix using some pymol settings ?
> Thank you in advance!
> J
>
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